{"id":"W2064604026","doi":"10.1093/nar/gkt1087","title":"TFBSshape: a motif database for DNA shape features of transcription factor binding sites","year":2013,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":128,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"National Institute of General Medical Sciences; National Human Genome Research Institute","keywords":"Biology; Motif (music); Transcription factor; Genetics; DNA binding site; DNA; Computational biology; Sequence motif; Transcription (linguistics); DNA-binding protein; Database; Promoter; Gene; Gene expression; Computer science","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006774353,0.002182661,0.001826938,0.003468242,0.0006697592,0.00106479,0.00265264,0.00129013,0.02105947],"category_scores_gemma":[0.002627664,0.0008741853,0.001277306,0.003309312,0.0002181041,0.001480212,0.001313612,0.001167272,0.01714681],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005196693,"about_ca_system_score_gemma":0.001125276,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002238905,"about_ca_topic_score_gemma":0.0048315,"domain_scores_codex":[0.9995011,0.00005995161,0.00008698684,0.0001417938,0.0001564451,0.00005366325],"domain_scores_gemma":[0.9994386,0.0001638592,0.00009939179,0.0001008902,0.000118761,0.0000785296],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.004495479,0.0004401412,0.01953519,0.008042827,0.0008525604,0.001309548,0.0007030352,0.01434356,0.2238777,0.01001191,0.4601352,0.2562529],"study_design_scores_gemma":[0.00157851,0.0006230172,0.02970421,0.0007161228,0.0005846357,0.002760655,0.0003572358,0.08316755,0.1205188,0.02074533,0.7387568,0.0004872698],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"dataset","genre_gemma":"dataset","genre_scores_codex":[0.0341625,0.003097763,0.1161975,0.0001672572,0.0001216749,0.0004695951,0.7217331,0.1177172,0.006333301],"genre_scores_gemma":[0.04589546,0.001057361,0.1061661,0.0001330877,0.00003957162,0.0009916653,0.8361223,0.006596032,0.002998369],"genre_candidate":"dataset","genre_consensus":"dataset","teacher_disagreement_score":0.02105947,"threshold_uncertainty_score":0.07045096,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04148482227225522,"score_gpt":0.3180629021143506,"score_spread":0.2765780798420954,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}